I had the same issue with my Model 3 (2018).
It rained heavily in the Bay Area, car was parked outside, level surface, for about 3-4 days over the holidays.
Opened the trunk to find it was sopping wet, with water sloshing around in the lower cargo area (underneath the lid). Mould on the lid, and later inside too...
Took it to Fremont service center (earliest available appointment) 2-3 weeks later. They said rear trunk seal was repaired. Repair and replacement of carpet, quoted at $573.
Car just got out of warranty in Dec...
I'm also concerned about other damage caused by this water leak (not just interior trim), and the water sloshing about in lower cargo area?
Anyone else experience downstream issues with the water sitting around, leaking through the wiring harness, or undercarriage?